title: Control ChIP-seq from spleen (ENCLB569CCQ)

description:
https://www.encodeproject.org/experiments/ENCSR889RIF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR889RIF
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB569CCQ
size range: 200-600

value: Control

value: spleen

value: tissue

value: ENCBS486GAC at ENCODE; https://www.encodeproject.org/ENCBS486GAC/


title: Nucleus Oprm1-Cre:H2BG Mu_O19

status: Public on Nov 01 2019

type: SRA

city: Stockholm

first: Konstantinos

last: Meletis

address: Solnavagen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt

library_source: transcriptomic

data_processing:
fastq files were aligned to mouse genome version mm10
 The alignments of reads towards the indicated genome assembly using SAMtools
The expression values were computed per gene as described in Ramsköld et al (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo
Clustering and marker identification was done using the Seurat package in R (versions 1.4.0 and 2.3.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene

molecule: total RNA

organism: Mus musculus

source_name: Oprm1-Cre nucleus striatum

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

tag: background strain

tag: genotype

tag: treatment

value: untreated


title: Normal 2

city: Shanghai

first: Sunwang

last: Xu

address: 160 Pujian Road, Shanghai, China

country: China

institute: Renji Hospital affiliated to Shanghai Jiao Tong University School of Medicine

description: processed data file: all.rpkm.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13.
HISAT2.1.0 mapping to reference genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: all.rpkm.txt: Tab-delimited text file includes RPKM values for each Sample.

organism: Homo sapiens

source_name: gallbladder tissue

growth_protocol: The fresh tumorous tissues and matched normal tissue were obtained from surgery.

extract_protocol:
Total RNA was extracted from tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The tissues were lysed in Trizol directly and do total RNA extraction.

tag: diagnosis

value: gallbladder cancer

tag: tissue

value: normal gallbladder

tag: individual


title: Nucleus Oprm1-Cre:H2BG Mu_P1


title: Nucleus Oprm1-Cre:H2BG Mu_O15


title: Tumor 3

description: processed data file: all.rpkm.txt

value: gallbladder tumor


title: Tumor 2

description: processed data file: all.rpkm.txt


title: Nucleus Oprm1-Cre:H2BG Mu_O12


title: Nucleus Oprm1-Cre:H2BG Mu_O14


title: Nucleus Oprm1-Cre:H2BG Mu_O13


title: Histone ChIP-seq from tibial nerve (ENCLB639OJW)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR860ZCZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR860ZCZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB639OJW
fragmentation methods: sonication (generic)
size range: 200-600

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

source_name: Homo sapiens male adult (37 years) tibial nerve tissue

extract_protocol: not provided

tag: antibody

value: tibial nerve

tag: description

value: EnTEX:Nerve - Tibial

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 37 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS647STW at ENCODE; https://www.encodeproject.org/ENCBS647STW/


title: Histone ChIP-seq from tibial nerve (ENCLB154VXF)

description:
https://www.encodeproject.org/experiments/ENCSR860ZCZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR860ZCZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB154VXF
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_O11


title: Tumor 1

description: processed data file: all.rpkm.txt


title: Histone ChIP-seq from suprapubic skin (ENCLB727WIS)

description:
https://www.encodeproject.org/experiments/ENCSR410BWN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR410BWN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB727WIS
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) suprapubic skin tissue

value: suprapubic skin

value: EnTEX:Skin - Not Sun Exposed (Suprapubic) updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS874KYB at ENCODE; https://www.encodeproject.org/ENCBS874KYB/


title: Nucleus Oprm1-Cre:H2BG Mu_O9


title: Nucleus Oprm1-Cre:H2BG Mu_O8


title: Nucleus Oprm1-Cre:H2BG Mu_O10


title: Histone ChIP-seq from suprapubic skin (ENCLB865TQH)

description:
https://www.encodeproject.org/experiments/ENCSR410BWN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR410BWN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB865TQH
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: Control ChIP-seq from spleen (ENCLB463GEG)

description:
https://www.encodeproject.org/experiments/ENCSR889RIF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR889RIF
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB463GEG
size range: 200-600

source_name: Homo sapiens male adult (37 years) spleen tissue

value: Control

value: spleen

value: ENCBS486GAC at ENCODE; https://www.encodeproject.org/ENCBS486GAC/


title: Nucleus Oprm1-Cre:H2BG Mu_O6

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_O7


title: Histone ChIP-seq from spleen (ENCLB513FZJ)

description:
https://www.encodeproject.org/experiments/ENCSR407UEE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR407UEE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB513FZJ
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from spleen (ENCLB150JHM)

description:
https://www.encodeproject.org/experiments/ENCSR407UEE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR407UEE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB150JHM
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_O2


title: Nucleus Oprm1-Cre:H2BG Mu_O1


title: Nucleus Oprm1-Cre:H2BG Mu_O5


title: Nucleus Oprm1-Cre:H2BG Mu_O4


title: 3P: Adjacent tissue

city: chongqing

first: Mengmeng

last: Jie

address: No. 83, Xinqiao street

institute: Third Military Medical University Xinqiao Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
In order to ensure the quality of information analysis, raw reads must be filtered to get clean reads. The subsequent analysis is based on clean reads.then mapped toGRCh38.p5 whole genome using hisat2
In RNA-seq analysis, we can estimate the level of gene expression by counting the sequencing sequences (reads) located in genomic regions or gene exons. Reads counts were positively correlated with gene length and sequence depth, as well as with the true expression level of the gene. The concept of FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is introduced to make the estimated gene expression levels of different genes and experiments comparable.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Stomach

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-seq library was prepared with approximately 2μg of total RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina(Kapa Biosystems, MA). Briefly, ribosomal RNA was removed from the total RNA. The ribosome-depleted RNA was incubated for 30 min at 37 °C with 10 units RNase R (Epicentre Technologies, USA).

treatment_protocol: All tissues were immediately preserved in liquid nitrogen.

value: Stomach

tag: cell type

value: Adjacent tissue


title: Nucleus Oprm1-Cre:H2BG Mu_O3


title: Nucleus Oprm1-Cre:H2BG Mu_N24


title: Patient 2 Kidney Homogenate

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

data_processing:
Preliminary sequencing results (bcl files) were converted to FASTQ files with Cell Ranger V3.0; R1 end, at the beginning of 16bp is CellBarcode sequence, then 10bp is UMI sequence, R2 end, we can truncate 151bp to 98bp
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Normalization and additional analysis by Seurat R package
Genome_build: GRCh38 for human data
Supplementary_files_format_and_content: the barcode, gene, expression matrix file of each sample

source_name: Kidney

extract_protocol:
We used 10x Genomics Chromium Single Cell 3′ Reagents Kit v2 user guide   to perform single cell suspension which were prepared before. Briefly, the  single-cell samples were passed through a 40μm cells strainer and counted using  a hemocytometer with trypan blue. Subsequently, the appropriate volume for each sample was calculated to  recover 10,000 cells. With the 10x protocol, we added the single cells, the Gel Beads and the  oils onto the 10x Genomics single-cell-A chip and run this machine. After  droplet generation, samples were transferred onto a PCR tube and reverse  transcription was performed using T100 Thermal Cycler (BIO-RAD). After the  reverse transcription, cDNA was recovered using Recovery Agent provided by 10x genomics  followed by a Silane DynaBead clean-up as outlined in the user guide. Purified  cDNA was amplified for 10 cycles before being cleaned up by using SPRIselect  beads. The samples were detected by Qubit2.0 Fluorometer (invitrogen) to  determine cDNA concentration.
10X Genomics Single Cell 3' v2 Reagent Kit

tag: subject id

value: Patient/donor 2

tag: subject status

value: normal

tag: sample type

value: Total Kidney Homogenate


title: Histone ChIP-seq from stomach (ENCLB124PMD)

description:
https://www.encodeproject.org/experiments/ENCSR843UEZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR843UEZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB124PMD
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) stomach tissue

value: stomach

value: male

value: adult

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS940XKF at ENCODE; https://www.encodeproject.org/ENCBS940XKF/


title: Patient 1 Kidney Homogenate

value: Patient/donor 1


title: Patient 3 Kidney Homogenate

value: Patient/donor 3


title: Normal 1

description: processed data file: all.rpkm.txt

value: gallbladder cancer

value: normal gallbladder


title: Nucleus Oprm1-Cre:H2BG Mu_N21

tag: background strain

tag: genotype

tag: treatment


title: Nucleus Oprm1-Cre:H2BG Mu_N23


title: Nucleus Oprm1-Cre:H2BG Mu_N22


title: Histone ChIP-seq from stomach (ENCLB352VUB)

description:
https://www.encodeproject.org/experiments/ENCSR843UEZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR843UEZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB352VUB
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: 2P: Adjacent tissue

tag: tissue

value: Stomach

value: Adjacent tissue


title: Nucleus Oprm1-Cre:H2BG Mu_N20

value: untreated


title: 2C: Gastric cancer

value: Gastric cancer


title: Nucleus Oprm1-Cre:H2BG Mu_N18


title: Nucleus Oprm1-Cre:H2BG Mu_N19


title: Nucleus Oprm1-Cre:H2BG Mu_N16


title: Histone ChIP-seq from prostate gland (ENCLB334HSR)

description:
https://www.encodeproject.org/experiments/ENCSR841AJO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR841AJO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB334HSR
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens male adult (37 years) prostate gland tissue

tag: antibody

value: prostate gland

value: EnTEX:Prostate updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS866WWM at ENCODE; https://www.encodeproject.org/ENCBS866WWM/


title: Nucleus Oprm1-Cre:H2BG Mu_N17


title: Histone ChIP-seq from prostate gland (ENCLB589JGX)

description:
https://www.encodeproject.org/experiments/ENCSR841AJO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR841AJO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB589JGX
fragmentation methods: sonication (generic)
size range: 200-600

tag: description

value: male

value: adult

value: 37 year

value: ENCBS985DZK at ENCODE; https://www.encodeproject.org/ENCBS985DZK/


title: 3C: Gastric cancer


title: Nucleus Oprm1-Cre:H2BG Mu_N12


title: 1C: Gastric cancer


title: Nucleus Oprm1-Cre:H2BG Mu_N10


title: Histone ChIP-seq from right atrium auricular region (ENCLB932LMW)

description:
https://www.encodeproject.org/experiments/ENCSR392WQN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR392WQN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB932LMW
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) right atrium auricular region tissue

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

tag: biosample encode accession

value: female

value: 51 year

value: Bradley Bernstein, Broad

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS524KBT at ENCODE; https://www.encodeproject.org/ENCBS524KBT/


title: Nucleus Oprm1-Cre:H2BG Mu_N14


title: Histone ChIP-seq from right atrium auricular region (ENCLB243BZU)

description:
https://www.encodeproject.org/experiments/ENCSR392WQN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR392WQN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB243BZU
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

tag: Sex

value: Kristin Ardlie


title: Histone ChIP-seq from prostate gland (ENCLB300SKT)

description:
https://www.encodeproject.org/experiments/ENCSR841AJO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR841AJO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB300SKT
fragmentation methods: none
size range: 200-600

tag: dev stage

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: MGC-803SiCirc-3

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HiSat2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Gastric cancer cells

growth_protocol: MGC-803 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS (100 mg/mL) and 1% penicillin-streptomycin (100 U/mL).

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MGC-803 cells were transfected with control and SiRNA-CircMRPS35.

tag: cell line

value: Gastric cancer cells


title: Nucleus Oprm1-Cre:H2BG Mu_N9

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_N15


title: MGC-803SiCirc-1


title: Nucleus Oprm1-Cre:H2BG Mu_N8


title: MGC-803SiCirc-2


title: Nucleus Oprm1-Cre:H2BG Mu_N7


title: Histone ChIP-seq from suprapubic skin (ENCLB781HGP)

description:
https://www.encodeproject.org/experiments/ENCSR836VZX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR836VZX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB781HGP
fragmentation methods: sonication (generic)
size range: 200-600

value: suprapubic skin

value: EnTEX:Skin - Not Sun Exposed (Suprapubic) updated Feb 2019 with updated term name and ID from DCC.

tag: age

tag: lab

value: ENCBS874KYB at ENCODE; https://www.encodeproject.org/ENCBS874KYB/


title: MGC-803NC-3

value: control


title: Nucleus Oprm1-Cre:H2BG Mu_N6


title: 1P: Adjacent tissue

value: Stomach

value: Adjacent tissue


title: Nucleus Oprm1-Cre:H2BG Mu_N5


title: MGC-803NC-2


title: Histone ChIP-seq from tibial nerve (ENCLB666AYU)

description:
https://www.encodeproject.org/experiments/ENCSR384MUF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR384MUF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB666AYU
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: male

value: adult

value: 37 year

tag: source

tag: link

value: ENCBS647STW at ENCODE; https://www.encodeproject.org/ENCBS647STW/


title: Histone ChIP-seq from tibial nerve (ENCLB259OSN)

description:
https://www.encodeproject.org/experiments/ENCSR384MUF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR384MUF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB259OSN
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: Bradley Bernstein, Broad


title: Nucleus Oprm1-Cre:H2BG Mu_N4

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt


title: Nucleus Oprm1-Cre:H2BG Mu_N13


title: Histone ChIP-seq from prostate gland (ENCLB726QGR)

description:
https://www.encodeproject.org/experiments/ENCSR841AJO/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR841AJO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB726QGR
fragmentation methods: sonication (generic)
size range: 200-600

value: prostate gland

value: EnTEX:Prostate updated Feb 2019 with updated term name and ID from DCC.

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS985DZK at ENCODE; https://www.encodeproject.org/ENCBS985DZK/


title: Nucleus Oprm1-Cre:H2BG Mu_N3

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_N11


title: Histone ChIP-seq from suprapubic skin (ENCLB819BNH)

description:
https://www.encodeproject.org/experiments/ENCSR836VZX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR836VZX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB819BNH
fragmentation methods: sonication (generic)
size range: 200-600

value: suprapubic skin

value: EnTEX:Skin - Not Sun Exposed (Suprapubic) updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS874KYB at ENCODE; https://www.encodeproject.org/ENCBS874KYB/


title: Nucleus Oprm1-Cre:H2BG Mu_N2


title: Nucleus Oprm1-Cre:H2BG Mu_M24


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB206JCK)

description:
https://www.encodeproject.org/experiments/ENCSR821VGC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR821VGC
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB206JCK
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS884JOD at ENCODE; https://www.encodeproject.org/ENCBS884JOD/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB996FXH)

description:
https://www.encodeproject.org/experiments/ENCSR821VGC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR821VGC
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB996FXH
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: adult


title: Nucleus Oprm1-Cre:H2BG Mu_N1


title: Histone ChIP-seq from suprapubic skin (ENCLB692EJO)

description:
https://www.encodeproject.org/experiments/ENCSR374XIN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR374XIN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB692EJO
fragmentation methods: sonication (generic)
size range: 200-600

value: 37 year


title: Nucleus Oprm1-Cre:H2BG Mu_M23


title: Nucleus Oprm1-Cre:H2BG Mu_M20


title: Chr2pos_M8_Left_CD3CD19Depleted

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 77 Massachusetts Ave

department: Chemistry

institute: Massachusetts Institute of Technology

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
to summarize:  1) Read 1 split into the first 12 base pairs, describing the cell barcode and 13-20th base pairs, encoding the unique molecular identifier (UMI)  2) cell barcodes, UMIs, and read 2 sequences with low base quality discarded, trimming for primer sequences or poly-T tails  3) read 2 alignd to mouse genome mm10 using STAR v2.5.2b with default parameters  4) Aligned sequences merged by cell barcode and UMI, sequences corresponding to barcodes wtih hamming edit distance 1 merged
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a tab delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

molecule: polyA RNA

source_name: Inguinal LN

growth_protocol: All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols of Harvard Medical School.

extract_protocol:
Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well method (Gierahn et al Nature Methods 2017)
Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well method (Gierahn et al Nature Methods 2017)

tag: side

value: Left

value: Nav1.8Cre/+; Rosa26LSL-ChR2-eYFP/+

tag: cell depletion type

value: CD3e/CD19 depleted

tag: animal number


title: Chr2pos_M8_Right_CD3CD19Depleted

value: Right


title: Histone ChIP-seq from right atrium auricular region (ENCLB689UKH)

description:
https://www.encodeproject.org/experiments/ENCSR817FGU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR817FGU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB689UKH
fragmentation methods: sonication (generic)
size range: 200-600

value: right atrium auricular region

value: tissue

value: EnTEX:Heart - Atrial Appendage

value: female

value: 51 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS524KBT at ENCODE; https://www.encodeproject.org/ENCBS524KBT/


title: Chr2pos_M7_Right_Undepleted

value: Undepleted


title: Nucleus Oprm1-Cre:H2BG Mu_M17

tag: background strain

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_M16

tag: genotype


title: Nucleus Oprm1-Cre:H2BG Mu_M15

tag: treatment


title: Nucleus Oprm1-Cre:H2BG Mu_M14


title: Chr2pos_M7_Right_CD3CD19Depleted


title: Control ChIP-seq from right atrium auricular region (ENCLB608SLW)

description:
https://www.encodeproject.org/experiments/ENCSR368NLE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR368NLE
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB608SLW
size range: 200-600

value: Control

value: adult


title: Chr2pos_M7_Left_Undepleted

value: Left


title: Chr2pos_M8_Right_Undepleted

value: Nav1.8Cre/+; Rosa26LSL-ChR2-eYFP/+


title: Nucleus Oprm1-Cre:H2BG Mu_M12


title: Nucleus Oprm1-Cre:H2BG Mu_M13


title: Nucleus Oprm1-Cre:H2BG Mu_M22


title: Nucleus Oprm1-Cre:H2BG Mu_M21


title: Control ChIP-seq from right atrium auricular region (ENCLB574WAZ)

description:
https://www.encodeproject.org/experiments/ENCSR368NLE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR368NLE
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB574WAZ
size range: 200-600

value: ENCBS088JMY at ENCODE; https://www.encodeproject.org/ENCBS088JMY/


title: Chr2pos_M8_Left_Undepleted


title: Nucleus Oprm1-Cre:H2BG Mu_M19


title: Nucleus Oprm1-Cre:H2BG Mu_M9


title: Nucleus Oprm1-Cre:H2BG Mu_M18


title: Histone ChIP-seq from suprapubic skin (ENCLB018WNM)

description:
https://www.encodeproject.org/experiments/ENCSR374XIN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR374XIN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB018WNM
fragmentation methods: sonication (generic)
size range: 200-600

value: suprapubic skin

value: EnTEX:Skin - Not Sun Exposed (Suprapubic) updated Feb 2019 with updated term name and ID from DCC.

value: male

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS874KYB at ENCODE; https://www.encodeproject.org/ENCBS874KYB/


title: Nucleus Oprm1-Cre:H2BG Mu_M8


title: Nucleus Oprm1-Cre:H2BG Mu_M10


title: Histone ChIP-seq from right atrium auricular region (ENCLB676ATP)

description:
https://www.encodeproject.org/experiments/ENCSR817FGU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR817FGU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB676ATP
fragmentation methods: sonication (generic)
size range: 200-600

value: right atrium auricular region

value: tissue

value: EnTEX:Heart - Atrial Appendage

value: female

value: 51 year

value: Bradley Bernstein, Broad


title: Nucleus Oprm1-Cre:H2BG Mu_M7

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_M6


title: Histone ChIP-seq from sigmoid colon (ENCLB209BAE)

description:
https://www.encodeproject.org/experiments/ENCSR807XUB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR807XUB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB209BAE
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) sigmoid colon tissue

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: adult

value: Kristin Ardlie

value: ENCBS365ZJJ at ENCODE; https://www.encodeproject.org/ENCBS365ZJJ/


title: Nucleus Oprm1-Cre:H2BG Mu_M5


title: Chr2pos_M2_Left_CD3CD19Depleted

value: Left

value: Nav1.8Cre/+; Rosa26LSL-ChR2-eYFP/+

value: CD3e/CD19 depleted


title: Nucleus Oprm1-Cre:H2BG Mu_M4


title: Chr2pos_M1_Right_CD3CD19Depleted

value: Right


title: Histone ChIP-seq from sigmoid colon (ENCLB235JFX)

description:
https://www.encodeproject.org/experiments/ENCSR807XUB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR807XUB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB235JFX
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Nucleus Oprm1-Cre:H2BG Mu_M3


title: Chr2pos_M7_Left_CD3CD19Depleted


title: Chr2pos_M1_Left_CD3CD19Depleted


title: Nucleus Oprm1-Cre:H2BG Mu_M1


title: Nucleus Oprm1-Cre:H2BG Mu_M11


title: Histone ChIP-seq from right atrium auricular region (ENCLB170WND)

description:
https://www.encodeproject.org/experiments/ENCSR361XMB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR361XMB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB170WND
fragmentation methods: none
size range: 200-600

value: right atrium auricular region

value: tissue

value: EnTEX:Heart - Atrial Appendage

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS088JMY at ENCODE; https://www.encodeproject.org/ENCBS088JMY/


title: Nucleus Oprm1-Cre:H2BG Mu_M2

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_L23


title: Nucleus Oprm1-Cre:H2BG Mu_L24


title: Histone ChIP-seq from right atrium auricular region (ENCLB822STS)

description:
https://www.encodeproject.org/experiments/ENCSR361XMB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR361XMB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB822STS
fragmentation methods: none
size range: 200-600

value: female

value: 51 year

value: Bradley Bernstein, Broad


title: Chr2pos_M2_Right_CD3CD19Depleted


title: Chr2neg_M6_Right_CD3CD19Depleted

value: Nav1.8Cre/+; Rosa26LSL-eYFP/+


title: Histone ChIP-seq from suprapubic skin (ENCLB889AAE)

description:
https://www.encodeproject.org/experiments/ENCSR362QYU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR362QYU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB889AAE
fragmentation methods: sonication (generic)
size range: 200-600

value: suprapubic skin

value: EnTEX:Skin - Not Sun Exposed (Suprapubic) updated Feb 2019 with updated term name and ID from DCC.

value: adult

value: Kristin Ardlie

value: ENCBS874KYB at ENCODE; https://www.encodeproject.org/ENCBS874KYB/


title: Nucleus Oprm1-Cre:H2BG Mu_L20


title: Nucleus Oprm1-Cre:H2BG Mu_L21


title: Nucleus Oprm1-Cre:H2BG Mu_L22


title: Chr2neg_M5_Right_Undepleted

value: Right

value: Undepleted


title: Histone ChIP-seq from suprapubic skin (ENCLB995JRB)

description:
https://www.encodeproject.org/experiments/ENCSR362QYU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR362QYU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB995JRB
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB381CUO)

description:
https://www.encodeproject.org/experiments/ENCSR353MNV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR353MNV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB381CUO
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) gastroesophageal sphincter tissue

value: gastroesophageal sphincter

value: tissue

value: EnTEX:Esophagus - Gastroesophageal Junction updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS727XQL at ENCODE; https://www.encodeproject.org/ENCBS727XQL/


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB064YYG)

description:
https://www.encodeproject.org/experiments/ENCSR353MNV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR353MNV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB064YYG
fragmentation methods: sonication (generic)
size range: 200-600


title: Chr2neg_M6_Left_CD3CD19Depleted

value: Left

value: CD3e/CD19 depleted


title: Nucleus Oprm1-Cre:H2BG Mu_L18

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt

value: untreated


title: Chr2neg_M5_Right_CD3CD19Depleted

value: Nav1.8Cre/+; Rosa26LSL-eYFP/+


title: Nucleus Oprm1-Cre:H2BG Mu_L19


title: MGC-803NC-1

tag: cell type

value: Gastric cancer cells

value: control


title: Nucleus Oprm1-Cre:H2BG Mu_L16


title: Chr2neg_M5_Left_Undepleted


title: Nucleus Oprm1-Cre:H2BG Mu_L17


title: Nucleus Oprm1-Cre:H2BG Mu_L15


title: Control ChIP-seq from tibial artery (ENCLB932VUP)

description:
https://www.encodeproject.org/experiments/ENCSR807FIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR807FIZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB932VUP
size range: 200-600

source_name: Homo sapiens male adult (37 years) tibial artery tissue

tag: antibody

value: Control

value: tibial artery

value: EnTEX:Artery - Tibial

value: adult

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Nucleus Oprm1-Cre:H2BG Mu_L14


title: Chr2neg_M5_Left_CD3CD19Depleted


title: Nucleus Oprm1-Cre:H2BG Mu_L13


title: Nucleus Oprm1-Cre:H2BG Mu_L11


title: Chr2neg_M3_Right_CD3CD19Depleted

value: Right


title: Nucleus Oprm1-Cre:H2BG Mu_L10


title: Histone ChIP-seq from breast epithelium (ENCLB284QRA)

description:
https://www.encodeproject.org/experiments/ENCSR793QCL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR793QCL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB284QRA
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) breast epithelium tissue

value: breast epithelium

value: tissue

tag: description

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS444JDU at ENCODE; https://www.encodeproject.org/ENCBS444JDU/


title: Chr2neg_M3_Left_CD3CD19Depleted

data_processing:
Reads aligned and pre-processed according to the DropSeq Computational Protocol v2.0 (https://github.com/broadinstitute/Drop-seq)
to summarize: 1) Read 1 split into the first 12 base pairs, describing the cell barcode and 13-20th base pairs, encoding the unique molecular identifier (UMI). 2) cell barcodes, UMIs, and read 2 sequences with low base quality discarded, trimming for primer sequences or poly-T tails. 3) read 2 aligned to mouse genome mm10 using STAR v2.5.2b with default parameters. 4) Aligned sequences merged by cell barcode and UMI, sequences corresponding to barcodes with hamming edit distance 1 were merged.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a tab delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

extract_protocol: Single-cell RNA capture, barcoding, and multiplexing according to the Seq-Well method (Gierahn et al Nature Methods 2017)

value: Left

value: Nav1.8Cre/+; Rosa26LSL-eYFP/+

value: CD3e/CD19 depleted


title: Nucleus Oprm1-Cre:H2BG Mu_L7

source_name: Oprm1-Cre nucleus striatum

value: untreated


title: DD_SeV

city: LOS ANGELES

first: Pinghui

last: Feng

department: Section of Infection and Immunity

institute: Herman Ostrow School of Dentistry, University of Southern California

description: Rela-/- MEF cells were 'reconstituted' with RelA-DD by lentivirus-mediated transduction. SeV Infection.

data_processing:
Illumina NextSeq 500 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into HISAT2 v2.1.0 for alignment into SAM files. SAM files are coverted into BAM files using Samtools v1.9.0
BAM files were imported into the StringTIe v1.3.6, and RPKM counts were calculated using R package edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: XLSX files include FPKM values for each Sample

source_name: Mouse Embrylonic Fibroblast

growth_protocol: Reconstituted' Rela-/- MEF cells were grown in DMEM/Hi-Glucose containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml)

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the KAPA RNA-Seq library kit.
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina adaptors prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x75 paired end flow cell.

treatment_protocol: Rela-/- MEF cells were 'reconstituted' with RelA-WT or RelA-DD by lentivirus-mediated transduction

value: RelA-DD mutant


title: DD_Mock

description: Rela-/- MEF cells were 'reconstituted' with RelA-DD by lentivirus-mediated transduction. No other treatment.


title: Nucleus Oprm1-Cre:H2BG Mu_L12


title: Nucleus Oprm1-Cre:H2BG Mu_L9


title: Histone ChIP-seq from Peyer's patch (ENCLB216XXO)

description:
https://www.encodeproject.org/experiments/ENCSR349GPJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR349GPJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB216XXO
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) Peyer's patch tissue

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum updated Feb 2019 with updated term name and ID from DCC.

tag: biosample encode accession

value: male

value: adult

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS388XLV at ENCODE; https://www.encodeproject.org/ENCBS388XLV/


title: Nucleus Oprm1-Cre:H2BG Mu_L5


title: Nucleus Oprm1-Cre:H2BG Mu_L8


title: Nucleus Oprm1-Cre:H2BG Mu_L6


title: WT_SeV

description: Rela-/- MEF cells were 'reconstituted' with RelA-WT by lentivirus-mediated transduction. SeV Infection.

value: RelA wild type


title: Histone ChIP-seq from breast epithelium (ENCLB777AFJ)

description:
https://www.encodeproject.org/experiments/ENCSR793QCL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR793QCL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB777AFJ
fragmentation methods: none
size range: 200-600

value: breast epithelium

value: tissue

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

tag: Sex

value: female

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Histone ChIP-seq from Peyer's patch (ENCLB629CUS)

description:
https://www.encodeproject.org/experiments/ENCSR349GPJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR349GPJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB629CUS
fragmentation methods: sonication (generic)
size range: 200-600

tag: dev stage


title: Histone ChIP-seq from tibial artery (ENCLB686DUU)

description:
https://www.encodeproject.org/experiments/ENCSR780CNW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR780CNW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB686DUU
fragmentation methods: none
size range: 200-600

value: tibial artery

value: EnTEX:Artery - Tibial

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Histone ChIP-seq from tibial artery (ENCLB592GXC)

description:
https://www.encodeproject.org/experiments/ENCSR780CNW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR780CNW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB592GXC
fragmentation methods: none
size range: 200-600


title: WT_Mock

description: Rela-/- MEF cells were 'reconstituted' with RelA-WT by lentivirus-mediated transduction. No other treatment.


title: Control ChIP-seq from tibial artery (ENCLB947HAN)

description:
https://www.encodeproject.org/experiments/ENCSR807FIZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR807FIZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB947HAN
size range: 200-600

value: Control


title: TF ChIP-seq from spleen (ENCLB145QXI)

description:
https://www.encodeproject.org/experiments/ENCSR343RJH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR343RJH
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB145QXI
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: spleen

value: ENCBS486GAC at ENCODE; https://www.encodeproject.org/ENCBS486GAC/


title: Nucleus Oprm1-Cre:H2BG Mu_L2

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_L3


title: Nucleus Oprm1-Cre:H2BG Mu_L1


title: RN2c_sgMef2c_2

city: Cold Spring Harbor

first: Yusuke

last: Tarumoto

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
X1072
RN2c_rosa_Mef2c_DESeq2_Normalized_expression_values.tabular

data_processing:
Sequencing reads were mapped into reference human genome hg19 or mm10 using HISAT2
Reads for protein coding genes were counted using FeatureCounts
Normalized and differentially expressed genes were analyzed using DESeq2
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: tabular, normalized RPKM

source_name: actue myeloid luekemia

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

treatment_protocol: Cells were lentivirally infected with sgRNA for knockout, or treated with DMSO or YKL-05-099 for 2 hrs

tag: cell line

value: RN2 Cas9 cell

tag: time point

value: day 2 after sgMef2c#2 guideRNA infection


title: TF ChIP-seq from spleen (ENCLB562QJE)

description:
https://www.encodeproject.org/experiments/ENCSR343RJH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR343RJH
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB562QJE
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) spleen tissue

value: male

value: adult

tag: age

value: 37 year

tag: lab

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Nucleus Oprm1-Cre:H2BG Mu_K23


title: Nucleus Oprm1-Cre:H2BG Mu_K24


title: RN2c_sgMef2c_1

description:
X1333
RN2c_rosa_Mef2c_DESeq2_Normalized_expression_values.tabular

value: day 2 after sgMef2c#1 guideRNA infection


title: Nucleus Oprm1-Cre:H2BG Mu_K20

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt


title: Histone ChIP-seq from prostate gland (ENCLB911TVH)

description:
https://www.encodeproject.org/experiments/ENCSR768PFZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR768PFZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB911TVH
fragmentation methods: none
size range: 200-600

value: prostate gland

value: tissue

value: EnTEX:Prostate updated Feb 2019 with updated term name and ID from DCC.

value: Bradley Bernstein, Broad

tag: source

tag: link

value: ENCBS866WWM at ENCODE; https://www.encodeproject.org/ENCBS866WWM/


title: Histone ChIP-seq from prostate gland (ENCLB182NZE)

description:
https://www.encodeproject.org/experiments/ENCSR768PFZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR768PFZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182NZE
fragmentation methods: none
size range: 200-600

value: Kristin Ardlie


title: RN2c_sgSIK3_e3

description:
X943
RN2c_rosa_Sik3_DESeq2_Normalized_expression_values.tabular

value: day 2 after sgSik3e3 guideRNA infection


title: Nucleus Oprm1-Cre:H2BG Mu_K22


title: Nucleus Oprm1-Cre:H2BG Mu_K21


title: Histone ChIP-seq from prostate gland (ENCLB501LTM)

description:
https://www.encodeproject.org/experiments/ENCSR768PFZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR768PFZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB501LTM
fragmentation methods: sonication (generic)
size range: 200-600

value: ENCBS985DZK at ENCODE; https://www.encodeproject.org/ENCBS985DZK/


title: Nucleus Oprm1-Cre:H2BG Mu_K17


title: Nucleus Oprm1-Cre:H2BG Mu_K19


title: RN2c_sgSIK3_e1

description:
X1094
RN2c_rosa_Sik3_DESeq2_Normalized_expression_values.tabular

value: day 2 after sgSik3e1 guideRNA infection


title: Nucleus Oprm1-Cre:H2BG Mu_K18

value: untreated


title: Control ChIP-seq from gastroesophageal sphincter (ENCLB443IKC)

description:
https://www.encodeproject.org/experiments/ENCSR343GIV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR343GIV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB443IKC
size range: 200-600

value: Control

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS727XQL at ENCODE; https://www.encodeproject.org/ENCBS727XQL/


title: RN2c_sgrosa26_2

description:
X1172
RN2c_rosa_Sik3_DESeq2_Normalized_expression_values.tabular

value: RN2 Cas9 cell

value: day 2 after sgrosa26 guideRNA infection


title: Histone ChIP-seq from prostate gland (ENCLB846VZG)

description:
https://www.encodeproject.org/experiments/ENCSR768PFZ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR768PFZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB846VZG
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: adult

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Nucleus Oprm1-Cre:H2BG Mu_L4


title: RN2_empty_YKL_2

description:
V5
RN2_empty_D_YKL_DESeq2_Normalized_expression_values.tabular

value: RN2 cell

value: 2 hr

tag: agent


title: Nucleus Oprm1-Cre:H2BG Mu_K12


title: Nucleus Oprm1-Cre:H2BG Mu_K14


title: Control ChIP-seq from gastroesophageal sphincter (ENCLB714UUB)

description:
https://www.encodeproject.org/experiments/ENCSR343GIV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR343GIV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB714UUB
size range: 200-600

value: tissue

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Nucleus Oprm1-Cre:H2BG Mu_K16


title: Nucleus Oprm1-Cre:H2BG Mu_K11


title: RN2c_sgrosa26_1

description:
X1291
RN2c_rosa_Sik3_DESeq2_Normalized_expression_values.tabular


title: RN2_empty_DMSO_2

description:
V3
RN2_empty_D_YKL_DESeq2_Normalized_expression_values.tabular

value: 0.1percent DMSO


title: Nucleus Oprm1-Cre:H2BG Mu_K9

value: untreated


title: RN2_empty_YKL_1

description:
V4
RN2_empty_D_YKL_DESeq2_Normalized_expression_values.tabular


title: Nucleus Oprm1-Cre:H2BG Mu_K8


title: Nucleus Oprm1-Cre:H2BG Mu_K10


title: Control ChIP-seq from tibial nerve (ENCLB781GWZ)

description:
https://www.encodeproject.org/experiments/ENCSR329HFV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR329HFV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB781GWZ
size range: 200-600

source_name: Homo sapiens male adult (37 years) tibial nerve tissue

value: Control

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: ENCBS647STW at ENCODE; https://www.encodeproject.org/ENCBS647STW/


title: Nucleus Oprm1-Cre:H2BG Mu_K7


title: RN2_empty_DMSO_1

description:
V2
RN2_empty_D_YKL_DESeq2_Normalized_expression_values.tabular


title: Nucleus Oprm1-Cre:H2BG Mu_K6


title: Nucleus Oprm1-Cre:H2BG Mu_K15


title: Nucleus Oprm1-Cre:H2BG Mu_K5


title: Nucleus Oprm1-Cre:H2BG Mu_K4


title: Histone ChIP-seq from upper lobe of left lung (ENCLB177PSJ)

description:
https://www.encodeproject.org/experiments/ENCSR276OPI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR276OPI
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB177PSJ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: ENCBS943JOF at ENCODE; https://www.encodeproject.org/ENCBS943JOF/


title: Nucleus Oprm1-Cre:H2BG Mu_K13

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt


title: Histone ChIP-seq from spleen (ENCLB265YIG)

description:
https://www.encodeproject.org/experiments/ENCSR506DCR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR506DCR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB265YIG
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: spleen

value: male

value: ENCBS511RRL at ENCODE; https://www.encodeproject.org/ENCBS511RRL/


title: Histone ChIP-seq from upper lobe of left lung (ENCLB934ZCF)

description:
https://www.encodeproject.org/experiments/ENCSR276OPI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR276OPI
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB934ZCF
fragmentation methods: sonication (generic)
size range: 200-600

value: adult

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Histone ChIP-seq from spleen (ENCLB580ETM)

description:
https://www.encodeproject.org/experiments/ENCSR426VHO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR426VHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB580ETM
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: Nucleus Oprm1-Cre:H2BG Mu_J24


title: Nucleus Oprm1-Cre:H2BG Mu_K2


title: Histone ChIP-seq from tibial artery (ENCLB686CQM)

description:
https://www.encodeproject.org/experiments/ENCSR764OHK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR764OHK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB686CQM
fragmentation methods: none
size range: 200-600

value: tibial artery

value: EnTEX:Artery - Tibial

value: Bradley Bernstein, Broad

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Nucleus Oprm1-Cre:H2BG Mu_J23

value: untreated


title: Histone ChIP-seq from spleen (ENCLB232MNV)

description:
https://www.encodeproject.org/experiments/ENCSR506DCR/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR506DCR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB232MNV
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie


title: Nucleus Oprm1-Cre:H2BG Mu_J22


title: Nucleus Oprm1-Cre:H2BG Mu_K1


title: Histone ChIP-seq from spleen (ENCLB588MBQ)

description:
https://www.encodeproject.org/experiments/ENCSR426VHO/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR426VHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB588MBQ
fragmentation methods: sonication (generic)
size range: 200-600


title: Control ChIP-seq from upper lobe of left lung (ENCLB426QBH)

description:
https://www.encodeproject.org/experiments/ENCSR746QZL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR746QZL
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB426QBH
size range: 200-600

value: Control


title: Histone ChIP-seq from spleen (ENCLB016GBE)

description:
https://www.encodeproject.org/experiments/ENCSR928BGP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR928BGP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB016GBE
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500


title: Nucleus Oprm1-Cre:H2BG Mu_J20


title: Nucleus Oprm1-Cre:H2BG Mu_J18


title: Nucleus Oprm1-Cre:H2BG Mu_J19


title: Nucleus Oprm1-Cre:H2BG Mu_J21


title: Control ChIP-seq from upper lobe of left lung (ENCLB472FJF)

description:
https://www.encodeproject.org/experiments/ENCSR746QZL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR746QZL
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB472FJF
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_J16


title: Control ChIP-seq from spleen (ENCLB574ZHH)

description:
https://www.encodeproject.org/experiments/ENCSR889RIF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR889RIF
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB574ZHH
size range: 200-600


title: Histone ChIP-seq from breast epithelium (ENCLB044AQE)

description:
https://www.encodeproject.org/experiments/ENCSR263XKR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR263XKR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB044AQE
fragmentation methods: sonication (generic)
size range: 200-600

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS444JDU at ENCODE; https://www.encodeproject.org/ENCBS444JDU/


title: Control ChIP-seq from spleen (ENCLB045GSF)

description:
https://www.encodeproject.org/experiments/ENCSR889RIF/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR889RIF
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB045GSF
size range: 200-600

value: spleen

value: male

value: adult

value: ENCBS511RRL at ENCODE; https://www.encodeproject.org/ENCBS511RRL/


title: Nucleus Oprm1-Cre:H2BG Mu_J14


title: Nucleus Oprm1-Cre:H2BG Mu_J15


title: Nucleus Oprm1-Cre:H2BG Mu_J17


title: Histone ChIP-seq from breast epithelium (ENCLB177PQL)

description:
https://www.encodeproject.org/experiments/ENCSR263XKR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR263XKR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB177PQL
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: Histone ChIP-seq from spleen (ENCLB780MOQ)

description:
https://www.encodeproject.org/experiments/ENCSR407UEE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR407UEE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB780MOQ
fragmentation methods: sonication (generic)
size range: 200-600

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Histone ChIP-seq from sigmoid colon (ENCLB442JMB)

description:
https://www.encodeproject.org/experiments/ENCSR734ZTQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR734ZTQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB442JMB
fragmentation methods: sonication (generic)
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: Bradley Bernstein, Broad

value: ENCBS365ZJJ at ENCODE; https://www.encodeproject.org/ENCBS365ZJJ/


title: Histone ChIP-seq from spleen (ENCLB860THE)

description:
https://www.encodeproject.org/experiments/ENCSR407UEE/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR407UEE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB860THE
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie


title: Nucleus Oprm1-Cre:H2BG Mu_J10

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_J13


title: Nucleus Oprm1-Cre:H2BG Mu_J12


title: Histone ChIP-seq from sigmoid colon (ENCLB748FQU)

description:
https://www.encodeproject.org/experiments/ENCSR734ZTQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR734ZTQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB748FQU
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_J9


title: Histone ChIP-seq from tibial nerve (ENCLB961WYY)

description:
https://www.encodeproject.org/experiments/ENCSR245VRR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR245VRR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB961WYY
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: ENCBS647STW at ENCODE; https://www.encodeproject.org/ENCBS647STW/


title: Histone ChIP-seq from tibial nerve (ENCLB121VDD)

description:
https://www.encodeproject.org/experiments/ENCSR245VRR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR245VRR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB121VDD
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_J8


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB611RRK)

description:
https://www.encodeproject.org/experiments/ENCSR731QXN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR731QXN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB611RRK
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS608MZC at ENCODE; https://www.encodeproject.org/ENCBS608MZC/


title: TF ChIP-seq from spleen (ENCLB957YPG)

description:
https://www.encodeproject.org/experiments/ENCSR343RJH/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR343RJH
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB957YPG
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: spleen

value: male

value: adult


title: Nucleus Oprm1-Cre:H2BG Mu_J6


title: Nucleus Oprm1-Cre:H2BG Mu_J5


title: Nucleus Oprm1-Cre:H2BG Mu_J7


title: Nucleus Oprm1-Cre:H2BG Mu_K3


title: Histone ChIP-seq from spleen (ENCLB658IZJ)

description:
https://www.encodeproject.org/experiments/ENCSR928BGP/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR928BGP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB658IZJ
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS511RRL at ENCODE; https://www.encodeproject.org/ENCBS511RRL/


title: TF ChIP-seq from right atrium auricular region (ENCLB644OJY)

description:
https://www.encodeproject.org/experiments/ENCSR232OFD/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR232OFD
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB644OJY
fragmentation methods: sonication (generic)
size range: 200-600

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: female

value: 51 year

value: Bradley Bernstein, Broad

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS524KBT at ENCODE; https://www.encodeproject.org/ENCBS524KBT/


title: Nucleus Oprm1-Cre:H2BG Mu_J3

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_J1


title: TF ChIP-seq from spleen (ENCLB585DLF)

description:
https://www.encodeproject.org/experiments/ENCSR343RJH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR343RJH
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB585DLF
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie


title: Nucleus Oprm1-Cre:H2BG Mu_J2


title: Nucleus Oprm1-Cre:H2BG Mu_J4


title: Control ChIP-seq from tibial nerve (ENCLB123XLB)

description:
https://www.encodeproject.org/experiments/ENCSR329HFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR329HFV
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB123XLB
size range: 200-600

value: Control

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: ENCBS647STW at ENCODE; https://www.encodeproject.org/ENCBS647STW/


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB022RBM)

description:
https://www.encodeproject.org/experiments/ENCSR731QXN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR731QXN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB022RBM
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus squamous epithelium

value: tissue

value: EnTEX:Esophagus - Mucosa updated Feb 2019 with updated term name and ID from DCC.

value: male

value: adult

value: ENCBS608MZC at ENCODE; https://www.encodeproject.org/ENCBS608MZC/


title: Histone ChIP-seq from tibial artery (ENCLB759PYF)

description:
https://www.encodeproject.org/experiments/ENCSR764OHK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR764OHK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB759PYF
fragmentation methods: none
size range: 200-600

value: tibial artery

value: EnTEX:Artery - Tibial

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Nucleus Oprm1-Cre:H2BG Mu_I24

value: untreated


title: TF ChIP-seq from right atrium auricular region (ENCLB556YLF)

description:
https://www.encodeproject.org/experiments/ENCSR232OFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR232OFD
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB556YLF
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: female

value: 51 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS524KBT at ENCODE; https://www.encodeproject.org/ENCBS524KBT/


title: Nucleus Oprm1-Cre:H2BG Mu_I23


title: Nucleus Oprm1-Cre:H2BG Mu_J11


title: Histone ChIP-seq from spleen (ENCLB085LCP)

description:
https://www.encodeproject.org/experiments/ENCSR091IRL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR091IRL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB085LCP
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: spleen

value: tissue

value: male

value: adult

value: ENCBS511RRL at ENCODE; https://www.encodeproject.org/ENCBS511RRL/


title: TF ChIP-seq from right atrium auricular region (ENCLB727RRO)

description:
https://www.encodeproject.org/experiments/ENCSR232OFD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR232OFD
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR368NLE
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB727RRO
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_I22


title: Nucleus Oprm1-Cre:H2BG Mu_I21


title: Histone ChIP-seq from upper lobe of left lung (ENCLB251XQG)

description:
https://www.encodeproject.org/experiments/ENCSR714FDJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR714FDJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251XQG
fragmentation methods: sonication (generic)
size range: 200-600

value: upper lobe of left lung

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS943JOF at ENCODE; https://www.encodeproject.org/ENCBS943JOF/


title: Nucleus Oprm1-Cre:H2BG Mu_I19

value: untreated


title: Histone ChIP-seq from spleen (ENCLB360XTO)

description:
https://www.encodeproject.org/experiments/ENCSR556QXD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR556QXD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB360XTO
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500


title: Histone ChIP-seq from upper lobe of left lung (ENCLB333EAZ)

description:
https://www.encodeproject.org/experiments/ENCSR714FDJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR714FDJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB333EAZ
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from spleen (ENCLB760LQA)

description:
https://www.encodeproject.org/experiments/ENCSR556QXD/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR556QXD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB760LQA
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_I16

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt


title: Histone ChIP-seq from stomach (ENCLB501CCX)

description:
https://www.encodeproject.org/experiments/ENCSR227DGG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR227DGG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB501CCX
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) stomach tissue

value: stomach

value: ENCBS940XKF at ENCODE; https://www.encodeproject.org/ENCBS940XKF/


title: Nucleus Oprm1-Cre:H2BG Mu_I20


title: Nucleus Oprm1-Cre:H2BG Mu_I18


title: Nucleus Oprm1-Cre:H2BG Mu_I17


title: Nucleus Oprm1-Cre:H2BG Mu_I15


title: Polysomal RNA-Arsenite-replicate-3

city: Vancouver

first: Syam Prakash

last: Somasekharan

state: BC

address: 2660 Oak St

country: Canada

institute: Vancouver Prostate Centre

data_processing:
Sequencing was performed on the Illumina NextSeq 500 with Paired End 42bp × 42bp reads. De-multiplexed read sequences were then aligned to the Homo sapiens UCSC hg19 reference sequence using STAR aligner. Assembly and differential expression were estimated using Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/) through bioinformatics apps available on Illumina Sequence Hub.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: PC-3 prostate cancer cell line

growth_protocol: PC-3 cells were cultured in RPMI medium

extract_protocol:
G3BP1 associated RNAs were extracted using APEX method; Total RNAs were extracted using TRIzol; Polysomal RNAs were extracted using Sucrose Gradient Polysomal Fractionation (SGPF)
Transcripts extracted from polysomes and G3BP1 complexes were depleted of the ribosomal RNA using Ribo-Zero (Illumina, San Diego, CA) and the sample quality was evaluated using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBNext Ultra II Stranded mRNA (New England Biolabs).

treatment_protocol: The cells were untreated or treated with arsenite

value: Prostate cancer

value: arsenite


title: Polysomal RNA-Arsenite-replicate-2


title: Nucleus Oprm1-Cre:H2BG Mu_I13


title: Polysomal RNA-untreated-replicate-3


title: Control ChIP-seq from Peyer's patch (ENCLB465GKV)

description:
https://www.encodeproject.org/experiments/ENCSR708OCZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR708OCZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB465GKV
size range: 200-600

value: Control

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum updated Feb 2019 with updated term name and ID from DCC.

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS388XLV at ENCODE; https://www.encodeproject.org/ENCBS388XLV/


title: Nucleus Oprm1-Cre:H2BG Mu_I14


title: Polysomal RNA-Arsenite-replicate-1


title: Nucleus Oprm1-Cre:H2BG Mu_I12


title: Histone ChIP-seq from stomach (ENCLB243FDB)

description:
https://www.encodeproject.org/experiments/ENCSR227DGG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR227DGG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR538MSN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB243FDB
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male

value: adult


title: Nucleus Oprm1-Cre:H2BG Mu_I11


title: Nucleus Oprm1-Cre:H2BG Mu_I10


title: Control ChIP-seq from Peyer's patch (ENCLB430AVC)

description:
https://www.encodeproject.org/experiments/ENCSR708OCZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR708OCZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB430AVC
size range: 200-600

value: 37 year


title: Polysomal RNA-untreated-replicate-2


title: Nucleus Oprm1-Cre:H2BG Mu_I9


title: Nucleus Oprm1-Cre:H2BG Mu_I8


title: Control ChIP-seq from Peyer's patch (ENCLB320VJN)

description:
https://www.encodeproject.org/experiments/ENCSR708OCZ/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR708OCZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB320VJN
size range: 200-600

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Nucleus Oprm1-Cre:H2BG Mu_I7


title: Nucleus Oprm1-Cre:H2BG Mu_I6


title: Nucleus Oprm1-Cre:H2BG Mu_I3


title: Total RNA-Arsenite-replicate-3

description: ControlUntreated_vs_ControlTreated_total RNA.gene_exp


title: Nucleus Oprm1-Cre:H2BG Mu_I5


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB863KOF)

description:
https://www.encodeproject.org/experiments/ENCSR706KWR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR706KWR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB863KOF
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS608MZC at ENCODE; https://www.encodeproject.org/ENCBS608MZC/


title: Nucleus Oprm1-Cre:H2BG Mu_I2

value: untreated


title: Polysomal RNA-untreated-replicate-1

value: Prostate cancer


title: Nucleus Oprm1-Cre:H2BG Mu_I1


title: Nucleus Oprm1-Cre:H2BG Mu_H24


title: Total RNA-Arsenite-replicate-2

value: arsenite


title: Nucleus Oprm1-Cre:H2BG Mu_H22


title: Nucleus Oprm1-Cre:H2BG Mu_I4


title: Nucleus Oprm1-Cre:H2BG Mu_H21


title: Nucleus Oprm1-Cre:H2BG Mu_H20


title: Total RNA-Untreated-replicate-3


title: Total RNA-Arsenite-replicate-1


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB338ANB)

description:
https://www.encodeproject.org/experiments/ENCSR188HXK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR188HXK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB338ANB
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS884JOD at ENCODE; https://www.encodeproject.org/ENCBS884JOD/


title: Total RNA-Untreated-replicate-2


title: Nucleus Oprm1-Cre:H2BG Mu_H19


title: Histone ChIP-seq from suprapubic skin (ENCLB316TKG)

description:
https://www.encodeproject.org/experiments/ENCSR702JHA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR702JHA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB316TKG
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) suprapubic skin tissue

value: suprapubic skin

value: EnTEX:Skin - Not Sun Exposed (Suprapubic) updated Feb 2019 with updated term name and ID from DCC.

value: Bradley Bernstein, Broad

value: ENCBS874KYB at ENCODE; https://www.encodeproject.org/ENCBS874KYB/


title: Total RNA-Untreated-replicate-1


title: Histone ChIP-seq from suprapubic skin (ENCLB600UBF)

description:
https://www.encodeproject.org/experiments/ENCSR702JHA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR702JHA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR531AUV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB600UBF
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male

value: Kristin Ardlie


title: Nucleus Oprm1-Cre:H2BG Mu_H18


title: Nucleus Oprm1-Cre:H2BG Mu_H17


title: G3BP1 arsenite interacting RNAs-replicate-3

description: GranuleCTRLarsenite_vs_GranuleG3BP1arsenite.gene_exp


title: Histone ChIP-seq from sigmoid colon (ENCLB953DLZ)

description:
https://www.encodeproject.org/experiments/ENCSR181HTE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR181HTE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB953DLZ
fragmentation methods: sonication (generic)
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: adult

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS365ZJJ at ENCODE; https://www.encodeproject.org/ENCBS365ZJJ/


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB615PCB)

description:
https://www.encodeproject.org/experiments/ENCSR706KWR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR706KWR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB615PCB
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS608MZC at ENCODE; https://www.encodeproject.org/ENCBS608MZC/


title: Nucleus Oprm1-Cre:H2BG Mu_H16

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_H15


title: Histone ChIP-seq from sigmoid colon (ENCLB470OEJ)

description:
https://www.encodeproject.org/experiments/ENCSR181HTE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR181HTE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB470OEJ
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_H14


title: Nucleus Oprm1-Cre:H2BG Mu_H13


title: Histone ChIP-seq from prostate gland (ENCLB305NNE)

description:
https://www.encodeproject.org/experiments/ENCSR690CSD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR690CSD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB305NNE
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) prostate gland tissue

value: prostate gland

value: EnTEX:Prostate updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS866WWM at ENCODE; https://www.encodeproject.org/ENCBS866WWM/


title: Nucleus Oprm1-Cre:H2BG Mu_H23


title: G3BP1 arsenite interacting RNAs-replicate-2

value: Prostate cancer

value: arsenite


title: Nucleus Oprm1-Cre:H2BG Mu_H12


title: G3BP1 arsenite interacting RNAs-replicate-1


title: CMV control Arsenite RNAs-replicate-3


title: Histone ChIP-seq from prostate gland (ENCLB314BYR)

description:
https://www.encodeproject.org/experiments/ENCSR690CSD/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR690CSD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB314BYR
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male

value: Bradley Bernstein, Broad


title: Nucleus Oprm1-Cre:H2BG Mu_H7

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt


title: Nucleus Oprm1-Cre:H2BG Mu_H6


title: CMV control Arsenite RNAs-replicate-1


title: Nucleus Oprm1-Cre:H2BG Mu_H8


title: Histone ChIP-seq from prostate gland (ENCLB044HQE)

description:
https://www.encodeproject.org/experiments/ENCSR155XVP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR155XVP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB044HQE
fragmentation methods: none
size range: 200-600

value: Kristin Ardlie


title: G3BP1 interacting RNAs-replicate-3


title: Histone ChIP-seq from prostate gland (ENCLB228ZZQ)

description:
https://www.encodeproject.org/experiments/ENCSR155XVP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR155XVP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB228ZZQ
fragmentation methods: sonication (generic)
size range: 200-600

value: adult

value: ENCBS985DZK at ENCODE; https://www.encodeproject.org/ENCBS985DZK/


title: Nucleus Oprm1-Cre:H2BG Mu_H4


title: Nucleus Oprm1-Cre:H2BG Mu_H5


title: Histone ChIP-seq from prostate gland (ENCLB692WPZ)

description:
https://www.encodeproject.org/experiments/ENCSR690CSD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR690CSD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB692WPZ
fragmentation methods: sonication (generic)
size range: 200-600

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: G3BP1 interacting RNAs-replicate-2


title: Nucleus Oprm1-Cre:H2BG Mu_H9


title: Nucleus Oprm1-Cre:H2BG Mu_H11


title: Nucleus Oprm1-Cre:H2BG Mu_H2


title: G3BP1 interacting RNAs-replicate-1


title: Histone ChIP-seq from prostate gland (ENCLB982RTN)

description:
https://www.encodeproject.org/experiments/ENCSR155XVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR155XVP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB982RTN
fragmentation methods: none
size range: 200-600


title: Histone ChIP-seq from prostate gland (ENCLB735NXH)

description:
https://www.encodeproject.org/experiments/ENCSR155XVP/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR155XVP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB735NXH
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_H10


title: Histone ChIP-seq from prostate gland (ENCLB643CHR)

description:
https://www.encodeproject.org/experiments/ENCSR690CSD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR690CSD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB643CHR
fragmentation methods: sonication (generic)
size range: 200-600


title: CMV control Arsenite RNAs-replicate-2


title: Nucleus Oprm1-Cre:H2BG Mu_G24


title: CMV control RNAs -replicate-3


title: CMV control RNAs -replicate-2


title: Nucleus Oprm1-Cre:H2BG Mu_G20


title: Nucleus Oprm1-Cre:H2BG Mu_G19


title: CMV control RNAs -replicate-1


title: Nucleus Oprm1-Cre:H2BG Mu_G22


title: Nucleus Oprm1-Cre:H2BG Mu_H3


title: Nucleus Oprm1-Cre:H2BG Mu_G16


title: Histone ChIP-seq from prostate gland (ENCLB009ZWM)

description:
https://www.encodeproject.org/experiments/ENCSR153NDQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR153NDQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB009ZWM
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_G17


title: Nucleus Oprm1-Cre:H2BG Mu_H1


title: Nucleus Oprm1-Cre:H2BG Mu_G14


title: Histone ChIP-seq from prostate gland (ENCLB817CHS)

description:
https://www.encodeproject.org/experiments/ENCSR153NDQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR153NDQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB817CHS
fragmentation methods: none
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_G13


title: BKOPAR4plusB

city: London

first: Jamie

middle: M

last: Kramer

state: Ontario

address: 1151 Richmond St.

department: Physiology and Pharmacology

institute: University of Western Ontario

description: rRNA-depleted total RNA

data_processing:
Basecalls performed using RTA v2
RNA-Seq reads were trimmed using Prinseq-lite 0.20.4 quality aware trimming
Reads were aligned to the H. sapiens genome using STAR 2.5.3a
Count tables were generated using HT-Seq Count v0.7.1 to count reads to genic features
Genome_build: Homo sapiens CRCh release 38
Supplementary_files_format_and_content: processed data files are raw count tables in .txt format.

source_name: HEK-293 cells

growth_protocol: Cells were maintained in DMEM with 10% fetal bovine serum, 1% penicillin-streptomycin, 1% sodium pyruvate, and 600 μg/mL geneticin.

extract_protocol:
Qiagen RNeasy mini kit
ScriptSeq complete kit

treatment_protocol: See "SAMPLES" section

value: beta-arrestin 1/2 double knockown expressing PAR4+YFP

value: Treated with 30μM AYPGKF-NH2


title: BKOPAR4plusA

description: rRNA-depleted total RNA


title: Histone ChIP-seq from prostate gland (ENCLB939CMV)

description:
https://www.encodeproject.org/experiments/ENCSR153NDQ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR153NDQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB939CMV
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_G12


title: BKOPAR4B

description: rRNA-depleted total RNA

value: Control treatment


title: BKOPAR4A

description: rRNA-depleted total RNA


title: Nucleus Oprm1-Cre:H2BG Mu_G10

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_G21


title: Nucleus Oprm1-Cre:H2BG Mu_G23


title: Nucleus Oprm1-Cre:H2BG Mu_G11


title: Nucleus Oprm1-Cre:H2BG Mu_G9


title: Nucleus Oprm1-Cre:H2BG Mu_G18